library(ggplot2)
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
"%&%" = function(a,b) paste(a,b,sep="")
for(pop in c('AFA-CAU','AFA-HIS','CAU-HIS')){
res <- read.table(pop %&% '_MESA_Nk-20.local-h2_gen-corr_EXP-SIM-0.2018-03-25.txt',header=T)
res <- dplyr::mutate(res,min.h2=ifelse(pop1.h2<pop2.h2,pop1.h2,pop2.h2), max.h2=ifelse(pop1.h2>pop2.h2,pop1.h2,pop2.h2))
print(summary(res))
print(ggplot(res, aes(x=rG,y=pop1.h2)) + geom_point() + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=pop1.se)) + geom_point() + ggtitle(pop))
print(ggplot(res, aes(x=pop1.h2,y=pop1.se)) + geom_point() + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=pop2.h2)) + geom_point() + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=pop2.se)) + geom_point() + ggtitle(pop))
print(ggplot(res, aes(x=pop2.h2,y=pop2.se)) + geom_point() + ggtitle(pop))
print(ggplot(res, aes(x=pop1.h2,y=pop2.h2,col=rG)) + geom_point()+scale_color_gradientn(colours = rainbow(4)) + ggtitle(pop))
print(ggplot(res, aes(x=pop1.h2,y=pop2.h2)) + stat_density_2d(aes(fill = ..level..), geom = "polygon") + ggtitle(pop))
print(ggplot(res, aes(x=pop1.h2,y=pop2.h2,col=log10(rG.se))) + geom_point() +scale_color_gradientn(colours = rainbow(4)) + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=log10(rG.se),col=min.h2)) + geom_point(alpha=0.5)+scale_color_gradientn(colours = rainbow(4)) + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=log10(rG.se),col=max.h2)) + geom_point(alpha=0.5)+scale_color_gradientn(colours = rainbow(4)) + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=log10(rG.se))) + stat_density_2d(aes(fill = ..level..), geom = "polygon") +
coord_cartesian(xlim=c(-1,1)) + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=log10(rG.se))) + stat_density_2d(geom = "point", aes(size = ..density..), n = 20, contour = FALSE) + ggtitle(pop))
print(ggplot(res, aes(x=rG)) + geom_density() + ggtitle(pop))
print(ggplot(res, aes(x=log10(rG.se))) + geom_density() + ggtitle(pop))
print(ggplot(res, aes(x=pop1.h2)) + geom_density() + ggtitle(pop))
print(ggplot(res, aes(x=pop2.h2)) + geom_density() + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=log10(rG.se))) + geom_bin2d() + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=log10(rG.se),col=pop1.h2)) + geom_point() + ggtitle(pop))
}
## pop.data N ensid
## AFA-CAU_MESA_Nk-20:9797 Min. :811 ENSG00000000419.8 : 1
## 1st Qu.:811 ENSG00000000457.8 : 1
## Median :811 ENSG00000000460.12: 1
## Mean :811 ENSG00000000938.8 : 1
## 3rd Qu.:811 ENSG00000000971.11: 1
## Max. :811 ENSG00000001036.8 : 1
## (Other) :9791
## gene chr start end
## A1BG : 1 chr1 :1062 Min. : 14363 Min. : 29370
## AAAS : 1 chr19 : 752 1st Qu.: 31191920 1st Qu.: 31230667
## AACS : 1 chr2 : 657 Median : 57647548 Median : 57698944
## AAED1 : 1 chr17 : 618 Mean : 72897113 Mean : 72948622
## AAGAB : 1 chr11 : 607 3rd Qu.:108320411 3rd Qu.:108507766
## AAK1 : 1 chr3 : 584 Max. :249200395 Max. :249214145
## (Other):9791 (Other):5517
## pop1.h2 pop1.se pop2.h2 pop2.se
## Min. :0.0000 Min. :0.0103 Min. :0.0000 Min. :0.0036
## 1st Qu.:0.0035 1st Qu.:0.0517 1st Qu.:0.0031 1st Qu.:0.0195
## Median :0.0457 Median :0.0658 Median :0.0273 Median :0.0269
## Mean :0.1074 Mean :0.0672 Mean :0.1135 Mean :0.0323
## 3rd Qu.:0.1468 3rd Qu.:0.0833 3rd Qu.:0.1369 3rd Qu.:0.0445
## Max. :0.9012 Max. :0.1371 Max. :0.9811 Max. :0.1020
## NA's :642 NA's :642 NA's :642 NA's :642
## rG rG.se min.h2 max.h2
## Min. :-1.0000 Min. : 0 Min. :0.0000 Min. :0.0000
## 1st Qu.:-1.0000 1st Qu.: 0 1st Qu.:0.0014 1st Qu.:0.0129
## Median : 0.0187 Median : 1 Median :0.0149 Median :0.0712
## Mean : 0.0138 Mean : 101988 Mean :0.0745 Mean :0.1465
## 3rd Qu.: 1.0000 3rd Qu.: 15 3rd Qu.:0.0789 3rd Qu.:0.2021
## Max. : 1.0000 Max. :611803315 Max. :0.9012 Max. :0.9811
## NA's :642 NA's :642 NA's :642 NA's :642
## Warning: Removed 642 rows containing missing values (geom_point).
## Warning: Removed 642 rows containing missing values (geom_point).
## Warning: Removed 642 rows containing missing values (geom_point).
## Warning: Removed 642 rows containing missing values (geom_point).
## Warning: Removed 642 rows containing missing values (geom_point).
## Warning: Removed 642 rows containing missing values (geom_point).
## Warning: Removed 642 rows containing missing values (geom_point).
## Warning: Removed 642 rows containing non-finite values (stat_density2d).
## Warning: Removed 642 rows containing missing values (geom_point).
## Warning: Removed 642 rows containing missing values (geom_point).
## Warning: Removed 642 rows containing missing values (geom_point).
## Warning: Removed 642 rows containing non-finite values (stat_density2d).
## Warning: Removed 642 rows containing non-finite values (stat_density2d).
## Warning: Removed 642 rows containing non-finite values (stat_density).
## Warning: Removed 642 rows containing non-finite values (stat_density).
## Warning: Removed 642 rows containing non-finite values (stat_density).
## Warning: Removed 642 rows containing non-finite values (stat_density).
## Warning: Removed 642 rows containing non-finite values (stat_bin2d).
## Warning: Removed 642 rows containing missing values (geom_point).
## pop.data N ensid
## AFA-HIS_MESA_Nk-20:9797 Min. :585 ENSG00000000419.8 : 1
## 1st Qu.:585 ENSG00000000457.8 : 1
## Median :585 ENSG00000000460.12: 1
## Mean :585 ENSG00000000938.8 : 1
## 3rd Qu.:585 ENSG00000000971.11: 1
## Max. :585 ENSG00000001036.8 : 1
## (Other) :9791
## gene chr start end
## A1BG : 1 chr1 :1062 Min. : 14363 Min. : 29370
## AAAS : 1 chr19 : 752 1st Qu.: 31191920 1st Qu.: 31230667
## AACS : 1 chr2 : 657 Median : 57647548 Median : 57698944
## AAED1 : 1 chr17 : 618 Mean : 72897113 Mean : 72948622
## AAGAB : 1 chr11 : 607 3rd Qu.:108320411 3rd Qu.:108507766
## AAK1 : 1 chr3 : 584 Max. :249200395 Max. :249214145
## (Other):9791 (Other):5517
## pop1.h2 pop1.se pop2.h2 pop2.se
## Min. :0.0000 Min. :0.0073 Min. :0.0000 Min. :0.0061
## 1st Qu.:0.0042 1st Qu.:0.0507 1st Qu.:0.0033 1st Qu.:0.0352
## Median :0.0468 Median :0.0641 Median :0.0427 Median :0.0471
## Mean :0.1041 Mean :0.0657 Mean :0.1270 Mean :0.0500
## 3rd Qu.:0.1400 3rd Qu.:0.0808 3rd Qu.:0.1767 3rd Qu.:0.0661
## Max. :0.8783 Max. :0.1518 Max. :0.9395 Max. :0.0990
## NA's :598 NA's :598 NA's :598 NA's :598
## rG rG.se min.h2 max.h2
## Min. :-1.0000 Min. : 0 Min. :0.0000 Min. :0.0000
## 1st Qu.:-0.9050 1st Qu.: 0 1st Qu.:0.0015 1st Qu.:0.0154
## Median : 0.1513 Median : 1 Median :0.0198 Median :0.0793
## Mean : 0.0839 Mean : 191081 Mean :0.0811 Mean :0.1500
## 3rd Qu.: 1.0000 3rd Qu.: 17 3rd Qu.:0.0959 3rd Qu.:0.2128
## Max. : 1.0000 Max. :714108060 Max. :0.8783 Max. :0.9395
## NA's :598 NA's :598 NA's :598 NA's :598
## Warning: Removed 598 rows containing missing values (geom_point).
## Warning: Removed 598 rows containing missing values (geom_point).
## Warning: Removed 598 rows containing missing values (geom_point).
## Warning: Removed 598 rows containing missing values (geom_point).
## Warning: Removed 598 rows containing missing values (geom_point).
## Warning: Removed 598 rows containing missing values (geom_point).
## Warning: Removed 598 rows containing missing values (geom_point).
## Warning: Removed 598 rows containing non-finite values (stat_density2d).
## Warning: Removed 598 rows containing missing values (geom_point).
## Warning: Removed 598 rows containing missing values (geom_point).
## Warning: Removed 598 rows containing missing values (geom_point).
## Warning: Removed 598 rows containing non-finite values (stat_density2d).
## Warning: Removed 598 rows containing non-finite values (stat_density2d).
## Warning: Removed 598 rows containing non-finite values (stat_density).
## Warning: Removed 598 rows containing non-finite values (stat_density).
## Warning: Removed 598 rows containing non-finite values (stat_density).
## Warning: Removed 598 rows containing non-finite values (stat_density).
## Warning: Removed 598 rows containing non-finite values (stat_bin2d).
## Warning: Removed 598 rows containing missing values (geom_point).
## pop.data N ensid
## CAU-HIS_MESA_Nk-20:9797 Min. :930 ENSG00000000419.8 : 1
## 1st Qu.:930 ENSG00000000457.8 : 1
## Median :930 ENSG00000000460.12: 1
## Mean :930 ENSG00000000938.8 : 1
## 3rd Qu.:930 ENSG00000000971.11: 1
## Max. :930 ENSG00000001036.8 : 1
## (Other) :9791
## gene chr start end
## A1BG : 1 chr1 :1062 Min. : 14363 Min. : 29370
## AAAS : 1 chr19 : 752 1st Qu.: 31191920 1st Qu.: 31230667
## AACS : 1 chr2 : 657 Median : 57647548 Median : 57698944
## AAED1 : 1 chr17 : 618 Mean : 72897113 Mean : 72948622
## AAGAB : 1 chr11 : 607 3rd Qu.:108320411 3rd Qu.:108507766
## AAK1 : 1 chr3 : 584 Max. :249200395 Max. :249214145
## (Other):9791 (Other):5517
## pop1.h2 pop1.se pop2.h2 pop2.se
## Min. :0.0000 Min. :0.0028 Min. :0.0000 Min. :0.0063
## 1st Qu.:0.0041 1st Qu.:0.0202 1st Qu.:0.0024 1st Qu.:0.0296
## Median :0.0340 Median :0.0279 Median :0.0353 Median :0.0400
## Mean :0.1106 Mean :0.0325 Mean :0.1032 Mean :0.0440
## 3rd Qu.:0.1368 3rd Qu.:0.0445 3rd Qu.:0.1319 3rd Qu.:0.0583
## Max. :0.9858 Max. :0.1170 Max. :0.9739 Max. :0.1060
## NA's :334 NA's :334 NA's :334 NA's :334
## rG rG.se min.h2 max.h2
## Min. :-1.0000 Min. : 0 Min. :0.0000 Min. :0.0000
## 1st Qu.:-0.7188 1st Qu.: 0 1st Qu.:0.0013 1st Qu.:0.0113
## Median : 0.0333 Median : 1 Median :0.0158 Median :0.0576
## Mean : 0.0210 Mean : 55764 Mean :0.0836 Mean :0.1302
## 3rd Qu.: 0.8230 3rd Qu.: 13 3rd Qu.:0.0925 3rd Qu.:0.1726
## Max. : 1.0000 Max. :273744693 Max. :0.9739 Max. :0.9858
## NA's :334 NA's :334 NA's :334 NA's :334
## Warning: Removed 334 rows containing missing values (geom_point).
## Warning: Removed 334 rows containing missing values (geom_point).
## Warning: Removed 334 rows containing missing values (geom_point).
## Warning: Removed 334 rows containing missing values (geom_point).
## Warning: Removed 334 rows containing missing values (geom_point).
## Warning: Removed 334 rows containing missing values (geom_point).
## Warning: Removed 334 rows containing missing values (geom_point).
## Warning: Removed 334 rows containing non-finite values (stat_density2d).
## Warning: Removed 334 rows containing missing values (geom_point).
## Warning: Removed 334 rows containing missing values (geom_point).
## Warning: Removed 334 rows containing missing values (geom_point).
## Warning: Removed 334 rows containing non-finite values (stat_density2d).
## Warning: Removed 334 rows containing non-finite values (stat_density2d).
## Warning: Removed 334 rows containing non-finite values (stat_density).
## Warning: Removed 334 rows containing non-finite values (stat_density).
## Warning: Removed 334 rows containing non-finite values (stat_density).
## Warning: Removed 334 rows containing non-finite values (stat_density).
## Warning: Removed 334 rows containing non-finite values (stat_bin2d).
## Warning: Removed 334 rows containing missing values (geom_point).
